There were 55 minutes on the stadium clock and a look of pure bewilderment on the faces of Tottenham’s defenders. They had just been shredded for the second time in three minutes by Serge Gnabry, Bayern Munich’s former Arsenal winger and, despite having carried the fight to the Bundesliga champions, they were staring at an irretrievable 4-1 deficit.

Remarkably, it was only the beginning of the pain for the manager, Mauricio Pochettino, and his team on a night when serious questions could be asked of their character. It has been a difficult season for them so far, with off-field issues from the summer hanging over into the opening weeks. Pochettino has repeatedly given the impression that he has been fighting with one hand tied behind his back. Here, he could do nothing to stop the onslaught as Gnabry and Bayern twisted the knife.

This was Gnabry’s night and he finished it with a four-goal haul, as Spurs wilted shamefully in the closing stages. For his hat-trick, he raced away from Jan Vertonghen to collect a long ball from the substitute Thiago Alcântara. He needed only two touches before he swept past Hugo Lloris and, after Robert Lewandowski had added Bayern’s sixth – the striker’s second of the evening – Gnabry beat Lloris yet again.

It is incredible to think that Gnabry once spent an unhappy loan spell at West Bromwich Albion under Tony Pulis in the 2015-16 season. He has developed into a world star since leaving the Premier League and he lit up a pulsating night with his pace and precision.

Gnabry’s opening goal was arguably the pick of the bunch; the first time he sent shockwaves around the stadium with his acceleration, which took him away from Serge Aurier’s slide tackle on halfway. In what felt like the blink of an eye, he had reached the edge of the Spurs area before he cut inside Toby Alderweireld and buried a shot into the far corner.

The result reinforced Bayern’s position at the top of Group B and it left Spurs with only one point from their two ties, after the 2-2 draw at Olympiakos a fortnight ago. They have it all to do in order to reach the knockout rounds for a third season in succession but the more immediate challenge is to come to terms with what was a humiliation. The scars will run deep for some time and the fear is that they could derail their season. In their 137-year history, Spurs have never conceded seven at home and never before have an English team been so badly beaten at home in Europe.

It felt like a trick of the imagination that Spurs had taken the lead through Son Heung-min; that they were the better team for the first 30 minutes and that Pochettino was not guilty of too much exaggeration when he said that he felt in his most upbeat mood of the season at half-time.

Spurs played with tempo at the outset and it was no surprise when Son put them in front, having gone close on two occasions in the early running. Both of those chances were laid on by Tanguy Ndombele, with the first being the clearer one. Son should have scored but he would make amends. Dele Alli pressed Corentin Tolisso and it was Moussa Sissoko who provided the incision. Son’s low finish had too much on it for Manuel Neuer.

Gnabry had shot too close to Lloris in the second minute – the first sign of his threat – and, although Bayern equalised through Joshua Kimmich’s beauty from distance, Spurs had their chances in the first half. Harry Kane rounded Neuer only for David Alaba to clear while Ndombele was denied by Neuer after Aurier’s clever pull-back.

Lewandowski’s goal on the stroke of half-time was the turning point and, if nothing else, it highlighted the slender nature of the margins at this level. Tolisso won the ball as he lay on the ground and Lewandowski took a touch, spun and fizzed a low shot into the corner from the edge of the area. Lewandowski has scored in every game of Bayern’s season – apart from the German Super Cup defeat against Borussia Dortmund, which has been their only loss. He is a byword for efficiency.

Niko Kovac, the Bayern manager, was compassionate in victory, saying that his team had simply taken an unusually high percentage of their chances and it should be noted that, after Kane’s penalty to make it 4-2, Sissoko and the substitute Christian Eriksen went close for Spurs. As strange as it sounds, Pochettino’s players believed they could fight back at that point.

Yet it was a Pochettino soundbite that hung heavy in the air. It was the one about his players giving up once Gnabry had completed his hat-trick. It was unacceptable. The boos from the home crowd rang out with feeling.